/*
 * 
 *                This source code is part of
 * 
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 *          GROningen MAchine for Chemical Simulations
 * 
 *                        VERSION 3.2.0
 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team,
 * check out http://www.gromacs.org for more information.

 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
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#ifdef HAVE_CONFIG_H
#include <config.h>
#endif

#include <string.h>
#include <ctype.h>
#include <math.h>

#include "sysstuff.h"
#include "smalloc.h"
#include "macros.h"
#include "statutil.h"
#include "maths.h"
#include "futil.h"
#include "index.h"
#include "copyrite.h"
#include "typedefs.h"
#include "xvgr.h"
#include "gstat.h"
#include "tpxio.h"
#include "vec.h"
#include "matio.h"
#include "gmx_ana.h"


int gmx_vanhove(int argc,char *argv[])
{
  const char *desc[] = {
    "g_vanhove computes the Van Hove correlation function.",
    "The Van Hove G(r,t) is the probability that a particle that is at r0",
    "at time zero can be found at position r0+r at time t.",
    "g_vanhove determines G not for a vector r, but for the length of r.",
    "Thus it gives the probability that a particle moves a distance of r",
    "in time t.",
    "Jumps across the periodic boundaries are removed.",
    "Corrections are made for scaling due to isotropic",
    "or anisotropic pressure coupling.",
    "[PAR]",
    "With option [TT]-om[tt] the whole matrix can be written as a function",
    "of t and r or as a function of sqrt(t) and r (option [TT]-sqrt[tt]).",
    "[PAR]",
    "With option [TT]-or[tt] the Van Hove function is plotted for one",
    "or more values of t. Option [TT]-nr[tt] sets the number of times,",
    "option [TT]-fr[tt] the number spacing between the times.",
    "The binwidth is set with option [TT]-rbin[tt]. The number of bins",
    "is determined automatically.",
    "[PAR]",
    "With option [TT]-ot[tt] the integral up to a certain distance",
    "(option [TT]-rt[tt]) is plotted as a function of time.",
    "[PAR]",
    "For all frames that are read the coordinates of the selected particles",
    "are stored in memory. Therefore the program may use a lot of memory.",
    "For options [TT]-om[tt] and [TT]-ot[tt] the program may be slow.",
    "This is because the calculation scales as the number of frames times",
    "[TT]-fm[tt] or [TT]-ft[tt].",
    "Note that with the [TT]-dt[tt] option the memory usage and calculation",
    "time can be reduced."
  };
  static int fmmax=0,ftmax=0,nlev=81,nr=1,fshift=0;
  static real sbin=0,rmax=2,rbin=0.01,mmax=0,rint=0;
  t_pargs pa[] = {
    { "-sqrt",    FALSE, etREAL,{&sbin},
      "Use sqrt(t) on the matrix axis which binspacing # in sqrt(ps)" },
    { "-fm",      FALSE, etINT, {&fmmax},
      "Number of frames in the matrix, 0 is plot all" },
    { "-rmax",    FALSE, etREAL, {&rmax},
      "Maximum r in the matrix (nm)" },
    { "-rbin",    FALSE, etREAL, {&rbin},
      "Binwidth in the matrix and for -or (nm)" },
    { "-mmax",    FALSE, etREAL, {&mmax},
      "Maximum density in the matrix, 0 is calculate (1/nm)" },
    { "-nlevels" ,FALSE, etINT,  {&nlev}, 
      "Number of levels in the matrix" },
    { "-nr",      FALSE, etINT, {&nr},
      "Number of curves for the -or output" },
    { "-fr",      FALSE, etINT, {&fshift},
      "Frame spacing for the -or output" },
    { "-rt",      FALSE, etREAL, {&rint},
      "Integration limit for the -ot output (nm)" },
    { "-ft",      FALSE, etINT, {&ftmax},
      "Number of frames in the -ot output, 0 is plot all" }
  };
#define NPA asize(pa)

  t_filenm fnm[] = { 
    { efTRX, NULL, NULL,  ffREAD },
    { efTPS, NULL, NULL,  ffREAD }, 
    { efNDX, NULL, NULL,  ffOPTRD },
    { efXPM, "-om", "vanhove", ffOPTWR },
    { efXVG, "-or", "vanhove_r", ffOPTWR },
    { efXVG, "-ot", "vanhove_t", ffOPTWR }
  };
#define NFILE asize(fnm)

  output_env_t oenv;
  const char *matfile,*otfile,*orfile;
  char     title[256];
  t_topology top;
  int      ePBC;
  matrix   boxtop,box,*sbox,avbox,corr;
  rvec     *xtop,*x,**sx;
  int      status,isize,nalloc,nallocn,natom;
  atom_id  *index;
  char     *grpname;
  int      nfr,f,ff,i,m,mat_nx=0,nbin=0,bin,mbin,fbin;
  real     *time,t,invbin=0,rmax2=0,rint2=0,d2;
  real     invsbin=0,matmax,normfac,dt,*tickx,*ticky;
  char     buf[STRLEN],**legend;
  real     **mat=NULL;
  int      *pt=NULL,**pr=NULL,*mcount=NULL,*tcount=NULL,*rcount=NULL;
  FILE     *fp;
  t_rgb    rlo={1,1,1}, rhi={0,0,0};

  CopyRight(stderr,argv[0]);

  parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
		    NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
  
  matfile = opt2fn_null("-om",NFILE,fnm);
  if (opt2parg_bSet("-fr",NPA,pa))
    orfile  = opt2fn("-or",NFILE,fnm);
  else
    orfile  = opt2fn_null("-or",NFILE,fnm);
  if (opt2parg_bSet("-rt",NPA,pa))
    otfile  = opt2fn("-ot",NFILE,fnm);
  else
    otfile  = opt2fn_null("-ot",NFILE,fnm);
  
  if (!matfile && !otfile && !orfile) {
    fprintf(stderr,
	    "For output set one (or more) of the output file options\n");
    exit(0);
  }
  
  read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xtop,NULL,boxtop,
		FALSE); 
  get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
  
  nalloc = 0;
  time = NULL;
  sbox = NULL;
  sx   = NULL;
  clear_mat(avbox);

  natom=read_first_x(oenv,&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
  nfr = 0;
  do {
    if (nfr >= nalloc) {
      nalloc += 100;
      srenew(time,nalloc);
      srenew(sbox,nalloc);
      srenew(sx,nalloc);
    }
    
    time[nfr] = t;
    copy_mat(box,sbox[nfr]);
    /* This assumes that the off-diagonal box elements
     * are not affected by jumps across the periodic boundaries.
     */
    m_add(avbox,box,avbox);
    snew(sx[nfr],isize);
    for(i=0; i<isize; i++)
     copy_rvec(x[index[i]],sx[nfr][i]);
    
    nfr++;
  } while (read_next_x(oenv,status,&t,natom,x,box));

  /* clean up */
  sfree(x);
  close_trj(status);
  
  fprintf(stderr,"Read %d frames\n",nfr);

  dt = (time[nfr-1] - time[0])/(nfr - 1);
  /* Some ugly rounding to get nice nice times in the output */
  dt = (int)(10000.0*dt + 0.5)/10000.0;

  invbin = 1.0/rbin;

  if (matfile) {
    if (fmmax <= 0 || fmmax >= nfr)
      fmmax = nfr - 1;
    snew(mcount,fmmax);
    nbin = (int)(rmax*invbin + 0.5);
    if (sbin == 0) {
      mat_nx = fmmax + 1;
    } else {
      invsbin = 1.0/sbin;
      mat_nx = sqrt(fmmax*dt)*invsbin + 1;
    }
    snew(mat,mat_nx);
    for(f=0; f<mat_nx; f++)
      snew(mat[f],nbin);
    rmax2 = sqr(nbin*rbin);
    /* Initialize time zero */
    mat[0][0] = nfr*isize;
    mcount[0] += nfr;
  } else {
    fmmax = 0;
  }
  
  if (orfile) {
    snew(pr,nr);
    nalloc = 0;
    snew(rcount,nr);
  }
  
  if (otfile) {
    if (ftmax <= 0)
      ftmax = nfr - 1;
    snew(tcount,ftmax);
    snew(pt,nfr);
    rint2 = rint*rint;
    /* Initialize time zero */
    pt[0] = nfr*isize;
    tcount[0] += nfr;
  } else {
    ftmax = 0;
  }

  msmul(avbox,1.0/nfr,avbox);
  for(f=0; f<nfr; f++) {
    if (f % 100 == 0)
      fprintf(stderr,"\rProcessing frame %d",f);
    /* Scale all the configuration to the average box */
    m_inv_ur0(sbox[f],corr);
    mmul_ur0(avbox,corr,corr);
    for(i=0; i<isize; i++) {
      mvmul_ur0(corr,sx[f][i],sx[f][i]);
      if (f > 0) {
	/* Correct for periodic jumps */
	for(m=DIM-1; m>=0; m--) {
	  while(sx[f][i][m] - sx[f-1][i][m] > 0.5*avbox[m][m])
	    rvec_dec(sx[f][i],avbox[m]);
	  while(sx[f][i][m] - sx[f-1][i][m] <= -0.5*avbox[m][m])
	    rvec_inc(sx[f][i],avbox[m]);
	}
      }
    }
    for(ff=0; ff<f; ff++) {
      fbin = f - ff;
      if (fbin <= fmmax || fbin <= ftmax) {
	if (sbin == 0)
	  mbin = fbin;
	else
	  mbin = (int)(sqrt(fbin*dt)*invsbin + 0.5);
	for(i=0; i<isize; i++) {
	  d2 = distance2(sx[f][i],sx[ff][i]);
	  if (mbin < mat_nx && d2 < rmax2) {
	    bin = (int)(sqrt(d2)*invbin + 0.5);
	    if (bin < nbin) {
	      mat[mbin][bin] += 1;
	    }
	  }
	  if (fbin <= ftmax && d2 <= rint2)
	    pt[fbin]++;
	}
	if (matfile)
	  mcount[mbin]++;
	if (otfile)
	  tcount[fbin]++;
      }
    }
    if (orfile) {
      for(fbin=0; fbin<nr; fbin++) {
	ff = f - (fbin + 1)*fshift;
	if (ff >= 0) {
	  for(i=0; i<isize; i++) {
	    d2 = distance2(sx[f][i],sx[ff][i]);
	    bin = (int)(sqrt(d2)*invbin);
	    if (bin >= nalloc) {
	      nallocn = 10*(bin/10) + 11;
	      for(m=0; m<nr; m++) {
		srenew(pr[m],nallocn);
		for(i=nalloc; i<nallocn; i++)
		  pr[m][i] = 0;
	      }
	      nalloc = nallocn;
	    }
	    pr[fbin][bin]++;
	  }
	  rcount[fbin]++;
	}
      }
    }
  }
  fprintf(stderr,"\n");
  
  if (matfile) {
    matmax = 0;
    for(f=0; f<mat_nx; f++) {
      normfac = 1.0/(mcount[f]*isize*rbin);
      for(i=0; i<nbin; i++) {
	mat[f][i] *= normfac;
	if (mat[f][i] > matmax && (f!=0 || i!=0))
	  matmax = mat[f][i];
      }
    }
    fprintf(stdout,"Value at (0,0): %.3f, maximum of the rest %.3f\n",
	    mat[0][0],matmax);
    if (mmax > 0)
      matmax = mmax;
    snew(tickx,mat_nx);
    for(f=0; f<mat_nx; f++) {
      if (sbin == 0)
	tickx[f] = f*dt;
      else
	tickx[f] = f*sbin;
    }
    snew(ticky,nbin+1);
    for(i=0; i<=nbin; i++)
      ticky[i] = i*rbin;
    fp = ffopen(matfile,"w");
    write_xpm(fp,MAT_SPATIAL_Y,"Van Hove function","G (1/nm)",
	      sbin==0 ? "time (ps)" : "sqrt(time) (ps^1/2)","r (nm)",
	      mat_nx,nbin,tickx,ticky,mat,0,matmax,rlo,rhi,&nlev);     
    ffclose(fp);
  }
  
  if (orfile) {
    fp = xvgropen(orfile,"Van Hove function","r (nm)","G (nm\\S-1\\N)",oenv);
    fprintf(fp,"@ subtitle \"for particles in group %s\"\n",grpname);
    snew(legend,nr);
    for(fbin=0; fbin<nr; fbin++) {
      sprintf(buf,"%g ps",(fbin + 1)*fshift*dt);
      legend[fbin] = strdup(buf);
    }
    xvgr_legend(fp,nr,legend,oenv);
    for(i=0; i<nalloc; i++) {
      fprintf(fp,"%g",i*rbin);
      for(fbin=0; fbin<nr; fbin++)
	fprintf(fp," %g",
		(real)pr[fbin][i]/(rcount[fbin]*isize*rbin*(i==0 ? 0.5 : 1)));
      fprintf(fp,"\n");
    }
    ffclose(fp);
  }
  
  if (otfile) {
    sprintf(buf,"Probability of moving less than %g nm",rint);
    fp = xvgropen(otfile,buf,"t (ps)","",oenv);
    fprintf(fp,"@ subtitle \"for particles in group %s\"\n",grpname);
    for(f=0; f<=ftmax; f++)
      fprintf(fp,"%g %g\n",f*dt,(real)pt[f]/(tcount[f]*isize));
    ffclose(fp);
  }

  do_view(oenv, matfile,NULL);
  do_view(oenv, orfile,NULL);
  do_view(oenv, otfile,NULL);

  thanx(stderr);
  
  return 0;
}
